Hi Dilip.

You have to place your files where the subject-directory points. If you dont change the directory yourself, this is under freesurfer/subjects.

For more info about recon all, see https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.mgh.ha...

Nina. ________________________________ Fra: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] på vegne af Dilip Puri [dilippuripuri@gmail.com] Sendt: 10. april 2017 07:46 Til: Freesurfer support list Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which directory. What are the command lines?

Hope for response.

Thanks Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Dilip

you need to run your image through recon-all.

cheers Bruce

On Sun, 9 Apr 2017, Dilip Puri wrote:

Hi all,

I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment HippoCampus.

My input file xyz.img and output file will be like xyz_seg.img which contains only hippocampus image it like Grond Truth image for my original input image.

Here is sample files including original and segmented mask link.

Even I am very new to FREESURFER so I don't know the procedure to reconstruct the images.

Kindly help me.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Dilip,

Try the mri_convert function to convert your images, so recon-all can read them: https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html ________________________________ Fra: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] på vegne af Dilip Puri [dilippuripuri@gmail.com] Sendt: 10. april 2017 10:02 Til: Freesurfer support list Emne: Re: [Freesurfer] segmentation help

Hi all,

Actually I've images in Analyze7.5 format(.img/.hdr). Can anyone help me to reconstruct('recon-all') for this format.

Thanks Dilip

On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen <njacob12@student.aau.dkmailto:njacob12@student.aau.dk> wrote: Hi Dilip.

You have to place your files where the subject-directory points. If you dont change the directory yourself, this is under freesurfer/subjects.

For more info about recon all, see https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.mgh.ha...

Nina. ________________________________ Fra: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] på vegne af Dilip Puri [dilippuripuri@gmail.commailto:dilippuripuri@gmail.com] Sendt: 10. april 2017 07:46 Til: Freesurfer support list Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which directory. What are the command lines?

Hope for response.

Thanks Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Dilip

you need to run your image through recon-all.

cheers Bruce

On Sun, 9 Apr 2017, Dilip Puri wrote:

Hi all,

I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment HippoCampus.

My input file xyz.img and output file will be like xyz_seg.img which contains only hippocampus image it like Grond Truth image for my original input image.

Here is sample files including original and segmented mask link.

Even I am very new to FREESURFER so I don't know the procedure to reconstruct the images.

Kindly help me.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

In this regard I've decided to change the dataset. We're going for ADNI Dataset http://adni.loni.usc.edu/ where I can find data in various format(nifti, mnc).

Is there any other dataset I can find labeled dataset for Hippocampus segmentation.

Thank you for helping me!

Dilip

On Mon, Apr 10, 2017 at 6:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

you can also just give them to recon-all directly. Analyze is a dangerous format to use however as it doesn't allow you to determine left from right. Hopefully you have some type of fiducial marker in the image (e.g. a vitamin E tablet)

cheers Bruce On Mon, 10 Apr 2017, Nina Jacobsen wrote:

Hi Dilip,

...

Try the mri_convert function to convert your images, so recon-all can read them: https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert .help.xml.html

---

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Fra: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] på vegne af Dilip Puri [dilippuripuri@gmail.com] Sendt: 10. april 2017 10:02 Til: Freesurfer support list Emne: Re: [Freesurfer] segmentation help

Hi all,

Actually I've images in Analyze7.5 format(.img/.hdr). Can anyone help me to reconstruct('recon-all') for this format.

Thanks Dilip

On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen njacob12@student.aau.dk wrote: Hi Dilip. You have to place your files where the subject-directory points. If you dont change the directory yourself, this is under freesurfer/subjects.

For more info about recon all,see https://surfer.nmr.mgh .harvard.edu/fswiki/recon-allhttps://surfer.nmr.m gh.harvard.edu/fswiki/recon-all

Nina.

---

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Fra: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] på vegne af Dilip Puri [dilippuripuri@gmail.com] Sendt: 10. april 2017 07:46 Til: Freesurfer support list Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which directory. What are the command lines?

Hope for response.

Thanks Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dilip

  you need to run your image through recon-all.

  cheers
  Bruce

  On Sun, 9 Apr 2017, Dilip Puri
  wrote:

  > Hi all,
  >
  > I've 200 analyze7.5 format images(OASIS Dataset) and I
  want to segment
  > HippoCampus.
  >
  > My input file xyz.img and output file will be like
  xyz_seg.img which
  > contains only hippocampus image it like Grond Truth
  image for my original
  > input image.
  >
  > Here is sample files including original and segmented
  mask link.
  >
  > Even I am very new to FREESURFER so I don't know the
  procedure to
  > reconstruct the images.
  >
  >
  > Kindly help me.
  >
  >

---

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---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.